Thanks for reply.
I have to do two different simulation at pH 5 & temperature 50 and pH 5
& temperature 55 degree celcius. I don't have to do for range of
temperature. So I was asking that is it possible to do MD at higher
temperature at pH 5.
Now I got the answer that constant pH is for 25 degree celcius.
Is there any option to do MD at above two condition.
On 2014-05-26 19:28, David A Case wrote:
> On Sun, May 25, 2014, Sangita Kachhap wrote:
>
>> Is it possible to do MD simulation at constant pH and temperature range 50-55 degree Celsius simultaneously?
>
> The thermostats in Amber allow you to specify a single (target) temperature,
> not a range of temperatures. If you really need a range, I'm guessing you
> would have to run a series of simulations at various temperatures of interest,
> and average the results. But a single simulation at the center of you
> temperature range would be a good place to start.
>
> The implicit solvent GB models in Amber were parameterized for 25 C; I don't
> know of any work testing these at higher temperature. If you are new to Amber
> (or to constant pH simulations) I'd recommend getting some experience with
> implicit solvent models first, before trying more difficult calculations.
>
> ....dac
>
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With regards
--
Sangita Kachhap
SRF
C/O Dr. Balvinder Singh
BIC
IMTECH
Links:
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Received on Mon May 26 2014 - 08:00:02 PDT
